prof. RNDr. Michal Otyepka, Ph.D.

2013

• Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment

  ŠPONER Jiří ŠPONEROVÁ Judit MLÁDEK Arnošt JURECKA Petr BANÁŠ Pavel OTYEPKA Michal

  Article in Periodical

  Biopolymers, year: 2013, volume: 99, edition: 12, DOI

• Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

  ZGARBOVA Marie LUQUE Javier F. ŠPONER Jiří CHEATHAM Thomas E III OTYEPKA Michal JUREČKA Petr

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2013, volume: 9, edition: 5, DOI

2012

• A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

  ZGARBOVÁ Marie JAVIER LUQUE F. ŠPONER Jiří OTYEPKA Michal JUREČKA Petr

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 9, DOI

• Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

  BANÁŠ Pavel MLÁDEK Arnošt OTYEPKA Michal ZGARBOVA Marie JURECKA Petr SVOZIL Daniel LANKAŠ Filip ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 7, DOI

• Molecular Dynamics Simulations of RNA Molecules

  ŠPONER Jiří OTYEPKA Michal BANÁŠ Pavel RÉBLOVÁ Kamila WALTER Nils

  Chapter of a book

  Innovations in Biomolecular Modeling and Simulations, edition: 1. vydání, year: 2012, number of pages: 27 s.

• Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study

  BANÁŠ Pavel SKLENOVSKY Petr WEDEKIND Joseph E ŠPONER Jiří OTYEPKA Michal

  Article in Periodical

  Journal of Physical Chemistry B, year: 2012, volume: 116, edition: 42, DOI

• MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels

  BERKA Karel HANÁK Ondřej SEHNAL David BANÁŠ Pavel NAVRÁTILOVÁ Veronika JAISWAL Deepti IONESCU Crina-Maria SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav OTYEPKA Michal

  Article in Periodical

  Nucleic Acids Research, year: 2012, volume: 40, edition: W1, DOI

• Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

  KREPL Miroslav ZGARBOVA Marie STADLBAUER Petr OTYEPKA Michal BANÁŠ Pavel KOČA Jaroslav CHEATHAM Thomas E. JURECKA Petr ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 7, DOI

• Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

  BEŠŠEOVÁ Ivana BANÁŠ Pavel KUEHROVA Petra KOSINOVA Pavlina OTYEPKA Michal ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2012, volume: 116, edition: 33, DOI

• The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

  ŠPONER Jiří MLÁDEK Arnošt ŠPONEROVÁ Judit SVOZIL Daniel ZGARBOVÁ Marie BANÁŠ Pavel JUREČKA Petr OTYEPKA Michal

  Article in Periodical

  PHYSICAL CHEMISTRY CHEMICAL PHYSICS, year: 2012, volume: 14, edition: 44, DOI